Directory /src/pkg/

Name      Synopsis
apps      Package apps provides simplified wrappers around computational biology tools that are typically operated from the command line.
     blast      Package blast provides functions and types to help with running any of the BLAST suite of programs.
     hhsuite      Package hhsuite provides convenient wrappers for running programs found in hhsuite like hhsearch, hhblits and hhmake.
     matt      Package matt provides a relatively bare bones blackbox for running Matt and easily gathering results like RMSD, core length and a p-value.
               rmsd      Example rmsd shows how to use the matt package to invoke Matt on multiple argument sets in parallel.
          bow-vs-matt      test bow-vs-matt compares the structural neighbors detected by a search on BOW vectors verus the structural neighbors detected by the Matt structural aligner.
          diff-kolodny-fragbag      diff-kolodny-fragbag is mostly a test program that compares the output of Kolodny's original implementation of Fragbag with the output of the Fragbag package.
          fragbag-ordering      test fragbag-ordering does an all-against-all search of the specified BOW database, and outputs the ordering of each search.
fragbag      Package fragbag provides interfaces for using fragment libraries along with several implementations of fragment libraries.
     bow      Package bow provides a representation of a bag-of-words (BOW) along with definitions of common operations.
     bowdb      Package bowdb provides functions for reading, writing and searching databases of Bowed values.
hhfrag      This package provides a Go implementation of Kalev and Habeck's HHfrag algorithm from their 2011 paper in Bioinformatics.
     fasta      Package fasta provides routines for reading and writing FASTA files and aligned FASTA files.
     hhr      Package hhr provides routines for reading (but not writing) hhr files, which are the output produced by hhsuite's hhsearch and hhblits programs.
     hmm      Package hhm parses hhm files generated by the HHsuite programs.
     msa      Package msa reads and writes multiple sequence alignments in FASTA, A2M or A3M formats.
     newick      Package newick provides facilities for reading and writing trees in the Newick format.
     pdbx      Package pdbx provides types and functions for reading PDBx/mmCIF formatted files conveniently.
seq      Package seq provides common types and operations for dealing with biological sequence data, with a bias toward amino acid sequences.
structure      Package rmsd implements a version of the Kabsch algorithm to compute the minimal RMSD between two equal length sets of atoms.
tools      Package tools provides command line tools that utilize the various repositories in the organization.
     bestfrag      bestfrag computes the best structural FragBag fragment that corresponds to the region provided.
     buildhhm      Example buildhhm shows how to construct an HHM using HHblits and HHmake from a single sequence FASTA file.
     clean-a3m      clean-a3m will read in all sequences in a given A3M file and overwrite the the given file with all non-empty sequences.
     pdb-rmsd      pdb-rmsd computes the RMSD between two sets of carbon-alpha ATOM records read from PDB files.
     pdbs-chains      Command pdbs-chains reads a file in the PDB Select format and outputs the list of PDB identifiers in the set.

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